Significantly improved how the NetCDF libraries and dependencies are …

…found.

buildscripts/build_all.sh

@@ -16,7 +16,30 @@
 SCRIPT_DIR=$(realpath $(dirname $0))
 ROOT_DIR=$(realpath ${SCRIPT_DIR}/..)
 BUILD_DIR="${ROOT_DIR}/build"
-PREFIX=${BUILD_DIR}/usr/local
+PREFIX=/usr/local
+
+# Parse arguments
+USTMT="Usage: ${0} [-d {./build}|/path/to/build] [-p {/usr/local}|/prefix/path]"
+IFORT=false
+PREFIX=/usr/local
+COMPILER=""
+while getopts ":c:d:" ARG; do
+    case "${ARG}" in
+    d)
+        BUILD_DIR="${OPTARG}"
+        ;;
+    p)
+        PREFIX="${OPTARG}"
+        ;;
+    :)      
+        echo "Error: -${OPTARG} requires an argument."
+        echo $USTMT
+        exit 1
+        ;;
+    *)
+        ;;
+    esac
+done
 
 mkdir -p ${BUILD_DIR}
 read -r OS ARCH < <($SCRIPT_DIR/get_platform.sh)

buildscripts/build_hdf5.sh

@@ -87,7 +87,13 @@ if [ $COMPILER = "GNU-Mac" ]; then
 fi
 COPTS="--disable-shared --enable-build-mode=production --disable-fortran --disable-java --disable-cxx --prefix=${PREFIX} --with-zlib=${PREFIX}"
 ./configure ${COPTS}
-make && make install
+make 
+if [ -w ${PREFIX} ]; then
+    make install
+else
+    sudo make install
+fi
+
 if [ $? -ne 0 ]; then
    printf "hdf5 could not be compiled.\n"
    exit 1

buildscripts/build_netcdf-c.sh

@@ -47,15 +47,15 @@ export FC=${FC}
 export F77=${F77}
 export CPP=${CPP}
 
-export HDF5_ROOT="${PREFIX}"
+export HDF5_ROOT=${HDF5_ROOT:-$PREFIX}
 export HDF5_LIBDIR="${HDF5_ROOT}/lib"
 export HDF5_INCLUDE_DIR="${HDF5_ROOT}/include"
 export HDF5_PLUGIN_PATH="${HDF5_LIBDIR}/plugin"
 export NCDIR="${PREFIX}"
 export NFDIR="${PREFIX}"
-export LD_LIBRARY_PATH="${PREFIX}/lib:${LD_LIBRARY_PATH}"
-export CPPFLAGS="${CPPFLAGS} -isystem ${PREFIX}/include"
-export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export LD_LIBRARY_PATH="${PREFIX}/lib:${HDF5_LIBDIR}:${LD_LIBRARY_PATH}"
+export CPPFLAGS="${CPPFLAGS} -isystem ${PREFIX}/include -isystem ${HDF5_INCLUDE_DIR}"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib -L${HDF5_LIBDIR}"
 export CPATH="${PREFIX}/include:${CPATH}"
 export CFLAGS="${CFLAGS} -Wno-unused-but-set-variable"
 
@@ -75,6 +75,7 @@ printf "CPPFLAGS: ${CPPFLAGS}\n"
 printf "CPATH: ${CPATH}\n"
 printf "LD_LIBRARY_PATH: ${LD_LIBRARY_PATH}\n"
 printf "LDFLAGS: ${LDFLAGS}\n"
+printf "HDF5_ROOT: ${HDF5_ROOT}\n"
 printf "*********************************************************\n"
 
 cd ${BUILD_DIR}/netcdf-c-*
@@ -84,34 +85,16 @@ if [ !  $COMPILER = "GNU-Mac" ]; then
 fi
 printf "COPTS: ${COPTS}\n"
 ./configure $COPTS
-make && make check && make install
-if [ $? -ne 0 ]; then
-   printf "netcdf-c could not be compiled."\n
-   exit 1
-fi
+make && make check 
 
-if [ $COMPILER = "Intel" ]; then 
-    export FCFLAGS="${CFLAGS} -standard-semantics"
+if [ -w ${PREFIX} ]; then
+    make install
 else
-    export FCFLAGS="${CFLAGS}"
+    sudo make install
 fi
-export FFLAGS=${CFLAGS}
 
-export LIBS="$(${PREFIX}/bin/nc-config --libs --static)"
-printf "\n"
-printf "*********************************************************\n"
-printf "*       BUILDING NETCDF-FORTRAN STATIC LIBRARY          *\n"
-printf "*********************************************************\n"
-cd ../netcdf-fortran-4.6.1
-./configure --disable-shared --with-pic --prefix=${PREFIX}  
-make && make check && make install
 if [ $? -ne 0 ]; then
-   printf "netcdf-fortran could not be compiled.\n"
+   printf "netcdf-c could not be compiled."\n
    exit 1
 fi
 
-printf "\n"
-printf "*********************************************************\n"
-printf "*             DEPENDENCIES ARE BUILT                    *\n"
-printf "*********************************************************\n"
-printf "Dependencys are installed to: ${PREFIX}\n\n"

buildscripts/build_netcdf-fortran.sh

@@ -82,7 +82,13 @@ printf "*********************************************************\n"
 
 cd ${BUILD_DIR}/netcdf-fortran-*
 ./configure --disable-shared --with-pic --disable-zstandard-plugin --prefix=${PREFIX}  
-make && make check && make install
+make && make check i
+if [ -w ${PREFIX} ]; then
+    make install
+else
+    sudo make install
+fi
+
 if [ $? -ne 0 ]; then
    printf "netcdf-fortran could not be compiled.\n"
    exit 1

buildscripts/build_swiftest.sh

@@ -49,6 +49,11 @@ printf "Dependency libraries in ${PREFIX}\n"
 
 export DEPDIR=$PREFIX
 export NETCDF_FORTRAN_HOME=$DEPDIR
+export HDF_ROOT=$PREFIX
+export HDF5_LIBDIR="${HDF5_ROOT}/lib"
+export HDF5_INCLUDE_DIR="${HDF5_ROOT}/include"
+export HDF5_PLUGIN_PATH="${HDF5_LIBDIR}/plugin"
+
 export LD_LIBRARY_PATH="${DEPDIR}/lib:${LD_LIBRARY_PATH}"
 export CPPFLAGS="${CPPFLAGS} -isystem ${DEPDIR}/include"
 export LDFLAGS="${LDFLAGS} -L${DEPDIR}/lib"
@@ -59,16 +64,7 @@ if [ $COMPILER = "GNU-Mac" ]; then
     export LDFLAGS="${LDFLAGS} -Wl,-no_compact_unwind"
     printf "MACOSX_DEPLOYMENT_TARGET: ${MACOSX_DEPLOYMENT_TARGET}\n"
 fi
-NFCFG="${DEPDIR}/bin/nf-config"
-if command -v $NFCFG &> /dev/null; then
-    export LIBS=$($NFCFG --flibs)
-else
-    printf "Error: Cannot find ${NFCFG}.\n"
-    printf "Is NetCDF-Fortran installed?\n"
-    exit 1
-fi
-export LDFLAGS="${LDFLAGS} -L${DEPDIR}/lib"
-export CFLAGS="-fPIC"
+
 export SKBUILD_CONFIGURE_OPTIONS="-DBUILD_SHARED_LIBS=OFF"
 
 if [ $COMPILER = "Intel" ]; then 

buildscripts/build_zlib.sh

@@ -73,7 +73,13 @@ printf "*********************************************************\n"
 cd ${BUILD_DIR}/zlib-*
 ./configure --prefix=${PREFIX} --static 
 make 
-make install
+
+if [ -w ${PREFIX} ]; then
+    make install
+else
+    sudo make install
+fi
+
 if [ $? -ne 0 ]; then
    printf "zlib could not be compiled.\n"
    exit 1

cmake/Modules/FindNETCDF.cmake

@@ -8,13 +8,91 @@
 # If not, see: https://www.gnu.org/licenses. 
 
 # - Finds the NetCDF libraries 
-set(NETCDF_FORTRAN_HOME $ENV{NETCDF_FORTRAN_HOME} CACHE STRING "Value of NetCDF library home directory")
-find_path(NETCDF_INCLUDE_DIR NAMES netcdf.mod HINTS ENV NETCDF_FORTRAN_HOME PATH_SUFFIXES include)
-find_library(NETCDF_FORTRAN_LIBRARY NAMES netcdff HINTS ENV NETCDF_FORTRAN_HOME PATH_SUFFIXES lib)
-find_library(NETCDF_LIBRARY NAMES netcdf HINTS ENV NETCDF_FORTRAN_HOME PATH_SUFFIXES lib)
 
-set(NETCDF_FOUND TRUE)
-# Note for posterity: When building static libraries, NETCDF_FORTRAN_LIBRARY must come *before* NETCDF_LIBRARY. Otherwise you get a bunch of "undefined reference to" errors
+FIND_PATH(NETCDF_INCLUDE_DIR 
+   NAMES netcdf.mod 
+   HINTS 
+      ENV NETCDF_INCLUDE_DIR 
+      ENV NETCDF_FORTRAN_HOME
+      ENV CPATH
+   PATH_SUFFIXES
+      include
+   REQUIRED
+)
 
-mark_as_advanced(NETCDF_LIBRARY NETCDF_FORTRAN_LIBRARY NETCDF_INCLUDE_DIR)
-set(NETCDF_LIBRARIES ${NETCDF_FORTRAN_LIBRARY} ${NETCDF_LIBRARY} CACHE STRING "NetCDF libraries")
+MESSAGE(STATUS "NetCDF-Fortran include directory: ${NETCDF_INCLUDE_DIR}")
+
+IF (BUILD_SHARED_LIBS) 
+   SET(NETCDFF "netcdff")
+ELSE ()
+   SET(NETCDFF "libnetcdff.a")
+   SET(NETCDF  "libnetcdf.a")
+ENDIF()
+
+FIND_LIBRARY(NETCDF_FORTRAN_LIBRARY 
+   NAMES ${NETCDFF} 
+   HINTS
+      ENV NETCDF_FORTRAN_HOME
+      ENV NETCDF_HOME
+      ENV LD_LIBRARY_PATH
+   PATH_SUFFIXES
+      lib
+      ${CMAKE_LIBRARY_ARCHITECTURE} 
+   REQUIRED
+)
+
+MESSAGE(STATUS "NetCDF-Fortran Library: ${NETCDF_FORTRAN_LIBRARY}")
+
+IF (BUILD_SHARED_LIBS)
+   SET(NETCDF_LIBRARIES ${NETCDF_FORTRAN_LIBRARY} CACHE STRING "NetCDF Fortran library")
+ELSE ()
+   FIND_LIBRARY(NETCDF_LIBRARY 
+      NAMES ${NETCDF} 
+      HINTS
+         ENV NETCDF_HOME
+         ENV LD_LIBRARY_PATH
+      PATH_SUFFIXES
+         lib
+         ${CMAKE_LIBRARY_ARCHITECTURE} 
+      REQUIRED
+   )
+
+   MESSAGE(STATUS "NetCDF-C Library: ${NETCDF_LIBRARY}")
+
+   FIND_PATH(NCBIN
+      NAMES nc-config
+      HINTS 
+         ENV NETCDF_HOME
+         ENV PATH
+      PATH_SUFFIXES
+         bin
+   )
+
+   IF (NCBIN) # The nc-config utility is available. Parse its output for unique flags
+      SET(CMD "${NCBIN}/nc-config")
+      LIST(APPEND CMD "--libs")
+      LIST(APPEND CMD "--static")
+      MESSAGE(STATUS "NetCDF configuration command: ${CMD}")
+      EXECUTE_PROCESS(COMMAND ${CMD} OUTPUT_VARIABLE EXTRA_FLAGS ERROR_VARIABLE ERR RESULT_VARIABLE RES OUTPUT_STRIP_TRAILING_WHITESPACE)
+      IF (EXTRA_FLAGS)
+         SEPARATE_ARGUMENTS(EXTRA_FLAGS NATIVE_COMMAND "${EXTRA_FLAGS}")
+         LIST(REMOVE_DUPLICATES EXTRA_FLAGS)
+         LIST(FILTER EXTRA_FLAGS EXCLUDE REGEX "netcdf+|-L+")
+         MESSAGE(STATUS "Extra library flags: ${EXTRA_FLAGS}")
+      ELSE ()
+         MESSAGE(STATUS "Cannot execute ${CMD}")
+         MESSAGE(STATUS "OUTPUT: ${EXTRA_FLAGS}")
+         MESSAGE(STATUS "RESUL : ${RES}")
+         MESSAGE(STATUS "ERROR : ${ERR}")
+         MESSAGE(FATAL_ERROR "Cannot configure NetCDF for static")
+      ENDIF ()
+   ELSE ()
+      MESSAGE(FATAL_ERROR "Cannot find nc-config")
+   ENDIF ()
+
+   # Note for posterity: When building static libraries, NETCDF_FORTRAN_LIBRARY must come *before* NETCDF_LIBRARY. Otherwise you get a bunch of "undefined reference to" errors
+   SET(NETCDF_LIBRARIES ${NETCDF_FORTRAN_LIBRARY} ${NETCDF_LIBRARY} ${EXTRA_FLAGS} CACHE STRING "NetCDF Fortran and dependant static libraries")
+ENDIF ()
+
+SET(NETCDF_FOUND TRUE)
+MARK_AS_ADVANCED(NETCDF_LIBRARIES NETCDF_INCLUDE_DIR)

cmake/Modules/SetFortranFlags.cmake

@@ -104,11 +104,13 @@ ELSEIF (COMPILER_OPTIONS STREQUAL "Intel")
         SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}"
                         Fortran "-pad"  # Intel
                                 "/Qpad" # Intel Windows
-
                         )
 ENDIF ()
 
 IF (NOT BUILD_SHARED_LIBS)
+        SET_COMPILE_FLAG(CMAKE_FORTRAN_FLAGS "${CMAKE_FORTRAN_FLAGS}"
+                        Fortran "-fPIC"
+                        )
 
         IF (COMPILER_OPTIONS STREQUAL "Intel")
                 # Use static Intel libraries

pyproject.toml

@@ -9,10 +9,8 @@ requires = [
 build-backend = "setuptools.build_meta"
 
 [tool.cibuildwheel.linux]
-environment = {SCRIPT_DIR="buildscripts", BUILD_DIR="build", PREFIX="/usr/local", SKBUILD_CONFIGURE_OPTIONS="-DBUILD_SHARED_LIBS=OFF", CFLAGS="-fPIC", CPPFLAGS="-isystem /usr/local/include", NETCDF_FORTRAN_HOME="/usr/local", LIBS="-lm -lz -ldl"}
+environment = {SKBUILD_CONFIGURE_OPTIONS="-DBUILD_SHARED_LIBS=OFF",CPATH="/usr:/usr/local",LD_LIBRARY_PATH="/usr/lib:/usr/lib64:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/aarch64-linux-gnu"}
 before-all = [
-    "yum install wget m4 doxygen -y",
-    "bash ${SCRIPT_DIR}/fetch_dependencies.sh -d ${BUILD_DIR}",
-    "bash ${SCRIPT_DIR}/build_dependencies.sh -c GNU-Linux -p ${PREFIX}"
+    "yum install netcdf-fortran-static netcdf-static hdf5-static -y",
 ]
 

setup.py

@@ -11,6 +11,8 @@
 """
 
 from skbuild import setup
+import os
+import subprocess
 
 with open('version.txt') as version_file:
     version = version_file.read().strip()

src/CMakeLists.txt

@@ -140,28 +140,21 @@ ELSEIF(BT STREQUAL "PROFILE")
    ADD_DEFINITIONS(-DPROFILE)
 ENDIF()
 
+# Define the executable name
+SET(SWIFTEST_DRIVER swiftest_driver)
+ADD_EXECUTABLE(${SWIFTEST_DRIVER} ${DRIVER_src})
+
 #####################################################
 # Add the needed libraries 
 #####################################################
 # Create a library from the source files, except the driver
 SET(SWIFTEST_LIBRARY swiftest)
 ADD_LIBRARY(${SWIFTEST_LIBRARY} ${SWIFTEST_src})
 
-# Define the executable name
-SET(SWIFTEST_DRIVER swiftest_driver)
-ADD_EXECUTABLE(${SWIFTEST_DRIVER} ${DRIVER_src})
-
-MESSAGE(STATUS "NetCDF Include directory: ${NETCDF_INCLUDE_DIR}")
 TARGET_INCLUDE_DIRECTORIES(${SWIFTEST_LIBRARY} PUBLIC ${NETCDF_INCLUDE_DIR})
 TARGET_INCLUDE_DIRECTORIES(${SWIFTEST_DRIVER} PUBLIC ${NETCDF_INCLUDE_DIR})
-
-IF (BUILD_SHARED_LIBS)
-    TARGET_LINK_LIBRARIES(${SWIFTEST_LIBRARY} PUBLIC ${NETCDF_LIBRARIES})
-    TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PUBLIC ${SWIFTEST_LIBRARY})
-ELSE ()
-    TARGET_LINK_LIBRARIES(${SWIFTEST_LIBRARY} PUBLIC ${NETCDF_LIBRARIES} $ENV{LIBS})
-    TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PUBLIC ${SWIFTEST_LIBRARY} ${NETCDF_LIBRARIES} $ENV{LIBS})
-ENDIF (BUILD_SHARED_LIBS)
+TARGET_LINK_LIBRARIES(${SWIFTEST_LIBRARY} PUBLIC ${NETCDF_LIBRARIES})
+TARGET_LINK_LIBRARIES(${SWIFTEST_DRIVER} PUBLIC ${SWIFTEST_LIBRARY} ${NETCDF_LIBRARIES})
 
 IF(USE_OPENMP OR USE_SIMD)
     SET_PROPERTY(TARGET ${SWIFTEST_LIBRARY} ${SWIFTEST_DRIVER} APPEND_STRING PROPERTY COMPILE_FLAGS  "${OpenMP_Fortran_FLAGS} ")